9UUS: The NuA3 histone acetyltransferase complex

The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail. Determined by electron microscopy at 3.2 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 6
Atoms: 10,835
Mol. weight: 252.01 kDa
Ligands: ACO, ZN
Released: 10 Dec 2025

Explore 9UUS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9UUS contains 55 α-helices and 42 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	108-110	3	1
β-strand	115-119	5	1
α-helix	122-125	4
α-helix	128-141	14
α-helix	154-166	13
α-helix	190-192	3
α-helix	195-198	4
α-helix	203-206	4
α-helix	215-226	12
α-helix	229-236	8
β-strand	275-276	2	2
β-strand	280-281	2	2
α-helix	292-295	4
β-strand	300-303	4	2
β-strand	308-310	3	2
α-helix	313-322	10
β-strand	335-336	2	3
β-strand	339-344	6	3
α-helix	352-361	10
β-strand	376	1	4
β-strand	378-385	8	3
α-helix	395-396	2
β-strand	397-404	8	3
β-strand	407	1	4
β-strand	414	1	5
β-strand	419-421	3	3
α-helix	430-444	15
β-strand	450	1	5
α-helix	459-463	5
α-helix	466-483	18
β-strand	493-494	2	6
β-strand	497	1	7
α-helix	499-506	8
α-helix	510-520	11
β-strand	523-524	2	8
β-strand	540-541	2	8
β-strand	542	1	9
α-helix	546-557	12
α-helix	566-568	3
α-helix	668-670	3
α-helix	680-688	9
α-helix	689-691	3
α-helix	694-695	2
β-strand	696-697	2	6

Chain B: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	7
β-strand	33	1	9
β-strand	92-93	2	2
α-helix	98-100	3
α-helix	114-120	7
α-helix	132-139	8
α-helix	162-172	11
α-helix	176-178	3
α-helix	191-198	8
α-helix	199-203	5
α-helix	209-227	19
α-helix	235-252	18
β-strand	275	1	10
β-strand	278	1	10
β-strand	280	1	11
α-helix	281-283	3
β-strand	291	1	11
α-helix	292-295	4
β-strand	320	1	12
β-strand	330-332	3	12
β-strand	333	1	13
β-strand	338-340	3	12
α-helix	341-346	6
β-strand	351-352	2	13
β-strand	361-362	2	13
α-helix	369-373	5
β-strand	387-388	2	14
β-strand	397-398	2	14
α-helix	400-406	7
β-strand	410-411	2	15
α-helix	417-422	6
β-strand	432-433	2	15
α-helix	436-438	3
α-helix	439-440	2
α-helix	447-464	18
β-strand	487	1	16
β-strand	493	1	16
α-helix	497-510	14
α-helix	516-532	17
α-helix	552-601	50

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	13-15	3
α-helix	23-41	19
α-helix	47-98	52
α-helix	100-102	3

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-52	41
α-helix	94-97	4
α-helix	100-109	10

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	179-186	8
α-helix	191-203	13
β-strand	211-214	4	1
β-strand	219-223	5	1
α-helix	224-226	3
α-helix	229-243	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	H	protein	21	Saccharomyces cerevisiae S288C	P61830 (AlphaFold model)
Histone acetyltransferase SAS3	A	protein	831	Saccharomyces cerevisiae S288C	P34218 (AlphaFold model)
NuA3 HAT complex component NTO1	B	protein	738	Saccharomyces cerevisiae S288C	Q12311 (AlphaFold model)
Protein YNG1	C	protein	219	Saccharomyces cerevisiae S288C	Q08465 (AlphaFold model)
Transcription initiation factor TFIID subunit 14	E	protein	244	Saccharomyces cerevisiae S288C	P35189
Chromatin modification-related protein EAF6	D	protein	113	Saccharomyces cerevisiae S288C	P47128

Sequence of entity 1 (H), FASTA

>9UUS_1 Histone H3 (chains H)
ARTKQTARKSTGGMAPRKQLA

Sequence of entity 2 (A), FASTA

>9UUS_2 Histone acetyltransferase SAS3 (chains A)
MSLTANDESPKPKKNALLKNLEIDDLIHSQFVRSDTNGHRTTRRLFNSDASISHRIRGSV
RSDKGLNKIKKGLISQQSKLASENSSQNIVNRDNKMGAVSFPIIEPNIEVSEELKVRIKY
DSIKFFNFERLISKSSVIAPLVNKNITSSGPLIGFQRRVNRLKQTWDLATENMEYPYSSD
NTPFRDNDSWQWYVPYGGTIKKMKDFSTKRTLPTWEDKIKFLTFLENSKSATYINGNVSL
CNHNETDQENEDRKKRKGKVPRIKNKVWFSQIEYIVLRNYEIKPWYTSPFPEHINQNKMV
FICEFCLKYMTSRYTFYRHQLKCLTFKPPGNEIYRDGKLSVWEIDGRENVLYCQNLCLLA
KCFINSKTLYYDVEPFIFYILTEREDTENHPYQNAAKFHFVGYFSKEKFNSNDYNLSCIL
TLPIYQRKGYGQFLMEFSYLLSRKESKFGTPEKPLSDLGLLTYRTFWKIKCAEVLLKLRD
SARRRSNNKNEDTFQQVSLNDIAKLTGMIPTDVVFGLEQLQVLYRHKTRSLSSLDDFNYI
IKIDSWNRIENIYKTWSSKNYPRVKYDKLLWEPIILGPSFGINGMMNLEPTALADEALTN
ETMAPVISNNTHIENYNNSRAHNKRRRRRRRSSEHKTSKLHVNNIIEPEVPATDFFEDTV
SSLTEYMCDYKNTNNDRLIYQAEKRVLESIHDRKGIPRSKFSTETHWELCFTIKNSETPL
GNHAARRNDTGISSLEQDEVENDVDTELYVGENAKEDEDEDEDFTLDDDIEDEQISEEND
EEEDTYEEDSDDDEDGKRKGQEQDENDIESHIRKERVRKRRKITLIEDDEE

Sequence of entity 3 (B), FASTA

>9UUS_3 NuA3 HAT complex component NTO1 (chains B)
KLREEKHFQDFYPDLNADTLLPFIVPLVETKDNSTDTDSDDISNRNNREIGSVKSVQTKE
LIFKGRVTTEPLVLKKNEVEFQKCKITTNELKGKKNPYCVRFNESFISRYYHINKVRNRK
SYKQQQKEFDGVEAPYFTKFSSKEAPNITISTSTKSAIQKFASISPNLVNFKPQYDMDEQ
DELYLHYLNKRYFKDQMSHEIFEILMTTLETEWFHIEKHIPSTNSLIARHNILRDCKNYE
LYGSDDGTGLSMDQACAVCLGTDSDNLNTIVFCDGCDIAVHQECYGIIFIPEGKWLCRRC
MISKNNFATCLMCPSHTGAFKQTDTGSWVHNICALWLPELYFSNLHYMEPIEGVQNVSVS
RWKLNCYICKKKMGACIQCFQRNCFTAYHVTCARRAGLYMSKGKCTIQELASNQFSQKYS
VESFCHKHAPRGWQTSIEGINKARKYFSLLSTLQTETPQHNEANDRTNSKFNKTIWKTPN
QTPVAPHVFAEILQKVVDFFGLANPPAGAFDICKYWSMKRELTGGTPLTACFENNSLGSL
TEEQVQTRIDFANDQLEDLYRLKELTTLVKKRTQASNSLSRSRKKVFDIVKSPQKYLLKI
NVLDIFIKSEQFKALERLVTEPKLLVILEKCKHCDFDTVQIFKEEIMHFFEVLETLPGAS
RILQTVSSKAKEQVTNLIGLIEHVDIKKLLSRDFIINDDKIEERPWSGPVIMEEEGLSDA
EELSAGEHRMLKLILNSG

Sequence of entity 4 (C), FASTA

>9UUS_4 Protein YNG1 (chains C)
MEHLANENSDSDIRYSFLSTLDHLPCELIRSLRLMQTIDLFKNEEDEPGMERACRDLLLV
ATYINDLVDDQIHFLKQHKKELEIQKSVTKNFNSSLENIKSKLTLEEPGAYKEPKLLLKI
NLKKAKSRERKESITSPTIGINQGDVTEGNNNQEEVYCFCRNVSYGPMVACDNPACPFEW
FHYGCVGLKQAPKGKWYCSKDCKEIANQRSKSKRQKRRK

Sequence of entity 5 (E), FASTA

>9UUS_5 Transcription initiation factor TFIID subunit 14 (chains E)
MVATVKRTIRIKTQQHILPEVPPVENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHP
TFANPNRTFTDPPFRIEEQGWGGFPLDISVFLLEKAGERKIPHDLNFLQESYEVEHVIQI
PLNKPLLTEELAKSGSTEETTANTGTIGKRRTTTNTTAEPKAKRAKTGSASTVKGSVDLE
KLAFGLTKLNEDDLVGVVQMVTDNKTPEMNVTNNVEEGEFIIDLYSLPEGLLKSLWDYVK
KNTE

Sequence of entity 6 (D), FASTA

>9UUS_6 Chromatin modification-related protein EAF6 (chains D)
MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHG
SKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Ligands and cofactors

ID	Name	Formula	Copies
ACO	Acetyl coenzyme *a	C23 H38 N7 O17 P3 S	1
ZN	Zinc ion	Zn	5

Primary citation

Mechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex. Shi, W., Zhao, L., Wang, Y. et al. Nat Commun (2025) 17:342-342. DOI 10.1038/s41467-025-67049-0 · PubMed

Other PDB entries of the same protein (UniProt P61830 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KMJ 1.4 Å, Crystal structure of Sth1 bromodomain in complex with H3K14Ac
7F3S 1.4 Å, Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
5D7E 1.9 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9ac
7F4A 2.0 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
1M1D 2.2 Å, Tetrahymena GCN5 with bound bisubstrate analog inhibitor
1QSN 2.2 Å, Crystal structure of tetrahymena GCN5 with bound coenzyme a and histone H3 peptide
2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
5IOK 2.22 Å, Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr

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